4GD3

Structure of E. coli hydrogenase-1 in complex with cytochrome b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of the O(2)-Tolerant Membrane-Bound Hydrogenase 1 from Escherichia coli in Complex with Its Cognate Cytochrome b.

Volbeda, A.Darnault, C.Parkin, A.Sargent, F.Armstrong, F.A.Fontecilla-Camps, J.C.

(2013) Structure 21: 184-190

  • DOI: 10.1016/j.str.2012.11.010
  • Primary Citation of Related Structures:  
    4GD3

  • PubMed Abstract: 
  • We report the 3.3 Å resolution structure of dimeric membrane-bound O(2)-tolerant hydrogenase 1 from Escherichia coli in a 2:1 complex with its physiological partner, cytochrome b. From the short distance between distal [Fe(4)S(4)] clusters, we predict rapid transfer of H(2)-derived electrons between hydrogenase heterodimers ...

    We report the 3.3 Å resolution structure of dimeric membrane-bound O(2)-tolerant hydrogenase 1 from Escherichia coli in a 2:1 complex with its physiological partner, cytochrome b. From the short distance between distal [Fe(4)S(4)] clusters, we predict rapid transfer of H(2)-derived electrons between hydrogenase heterodimers. Thus, under low O(2) levels, a functional active site in one heterodimer can reductively reactivate its O(2)-exposed counterpart in the other. Hydrogenase 1 is maximally expressed during fermentation, when electron acceptors are scarce. These conditions are achieved in the lower part of the host's intestinal tract when E. coli is soon to be excreted and undergo an anaerobic-to-aerobic metabolic transition. The apparent paradox of having an O(2)-tolerant hydrogenase expressed under anoxia makes sense if the enzyme functions to keep intracellular O(2) levels low by reducing it to water, protecting O(2)-sensitive enzymes during the transition. Cytochrome b's main role may be anchoring the hydrogenase to the membrane.


    Related Citations: 
    • X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli.
      Volbeda, A., Amara, P., Darnault, C., Mouesca, J.M., Parkin, A., Roessler, M.M., Armstrong, F.A., Fontecilla-Camps, J.C.
      (2012) Proc Natl Acad Sci U S A 109: 5305

    Organizational Affiliation

    Metalloproteins Unit, Institut de Biologie Structurale J.-P. Ebel CEA-CNRS-Université Joseph Fourier, UMR 5075, 41 rue Jules Horowitz, 38027 Grenoble, France. Electronic address: juan.fontecilla@ibs.fr.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hydrogenase-1 small chainE [auth Q], G [auth R], A [auth S], C [auth T]335Escherichia coli K-12Mutation(s): 1 
Gene Names: b0972hyaAJW0954
EC: 1.12.99.6
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
O2-tolerant Hydrogenase-1 in complex with cytochrome b
Find proteins for P69739 (Escherichia coli (strain K12))
Explore P69739 
Go to UniProtKB:  P69739
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hydrogenase-1 large chainF [auth J], H [auth K], B [auth L], D [auth M]582Escherichia coli K-12Mutation(s): 0 
Gene Names: b0973hyaBJW0955
EC: 1.12.99.6
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
O2-tolerant Hydrogenase-1 in complex with cytochrome b
Find proteins for P0ACD8 (Escherichia coli (strain K12))
Explore P0ACD8 
Go to UniProtKB:  P0ACD8
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ni/Fe-hydrogenase 1 B-type cytochrome subunitI [auth A], J [auth B]235Escherichia coli K-12Mutation(s): 0 
Gene Names: b0974hyaCJW0956
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
O2-tolerant Hydrogenase-1 in complex with cytochrome b
Find proteins for P0AAM1 (Escherichia coli (strain K12))
Explore P0AAM1 
Go to UniProtKB:  P0AAM1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
UA [auth A], WA [auth B]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
LMT
Query on LMT

Download Ideal Coordinates CCD File 
OA [auth R], VA [auth A], W [auth T], XA [auth B]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
CA [auth Q], DA [auth Q], K [auth S], L [auth S], LA [auth R], MA [auth R], T, U [auth T]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F4S
Query on F4S

Download Ideal Coordinates CCD File 
EA [auth Q], M [auth S], NA [auth R], V [auth T]FE4-S3 CLUSTER
Fe4 S3
QQACTBFBZNWJMV-UHFFFAOYSA-N
 Ligand Interaction
FCO
Query on FCO

Download Ideal Coordinates CCD File 
HA [auth J], P [auth L], QA [auth K], Y [auth M]CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
IA [auth J], Q [auth L], RA [auth K], Z [auth M]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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BA [auth M] , FA [auth Q] , GA [auth Q] , KA [auth J] , N [auth S] , O [auth S] , PA [auth K] , S [auth L] , 
BA [auth M],  FA [auth Q],  GA [auth Q],  KA [auth J],  N [auth S],  O [auth S],  PA [auth K],  S [auth L],  TA [auth K],  X [auth M]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth M], JA [auth J], R [auth L], SA [auth K]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126α = 90
b = 165.3β = 90
c = 212.8γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-02
    Type: Initial release
  • Version 1.1: 2013-01-09
    Changes: Database references
  • Version 1.2: 2013-01-30
    Changes: Database references